cleanUpdTSeq

DOI: 10.18129/B9.bioc.cleanUpdTSeq  

cleanUpdTSeq cleans up artifacts from polyadenylation sites from oligo(dT)-mediated 3' end RNA sequending data

Bioconductor version: Release (3.17)

This package implements a Naive Bayes classifier for accurately differentiating true polyadenylation sites (pA sites) from oligo(dT)-mediated 3' end sequencing such as PAS-Seq, PolyA-Seq and RNA-Seq by filtering out false polyadenylation sites, mainly due to oligo(dT)-mediated internal priming during reverse transcription. The classifer is highly accurate and outperforms other heuristic methods.

Author: Sarah Sheppard, Haibo Liu, Jianhong Ou, Nathan Lawson, Lihua Julie Zhu

Maintainer: Jianhong Ou <Jianhong.Ou at duke.edu>; Lihua Julie Zhu <Julie.Zhu at umassmed.edu>

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("cleanUpdTSeq")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("cleanUpdTSeq")

 

HTML	R Script	cleanUpdTSeq Vignette
PDF		Reference Manual
Text		NEWS

Details

biocViews	3' end sequencing, Sequencing, Software, internal priming, polyadenylation site
Version	1.38.0
In Bioconductor since	BioC 2.13 (R-3.0) (10 years)
License	GPL-2
Depends	R (>= 3.5.0), BSgenome.Drerio.UCSC.danRer7, methods
Imports	BSgenome, GenomicRanges, seqinr, e1071, Biostrings, GenomeInfoDb, IRanges, utils, stringr, stats, S4Vectors
LinkingTo
Suggests	BiocStyle, rmarkdown, knitr, RUnit, BiocGenerics(>= 0.1.0)
SystemRequirements
Enhances
URL
Depends On Me
Imports Me	InPAS
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	cleanUpdTSeq_1.38.0.tar.gz
Windows Binary	cleanUpdTSeq_1.38.0.zip (64-bit only)
macOS Binary (x86_64)	cleanUpdTSeq_1.38.0.tgz
macOS Binary (arm64)	cleanUpdTSeq_1.38.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/cleanUpdTSeq
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/cleanUpdTSeq
Bioc Package Browser	https://code.bioconductor.org/browse/cleanUpdTSeq/
Package Short Url	https://bioconductor.org/packages/cleanUpdTSeq/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.17	Source Archive